Abstract
BackgroundThe two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU×IB) were generated. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays.ResultsLoin muscle chemical composition showed significant differences between genetic types in intramuscular fat content (6.1% vs. 4.3% in IB and DUxIB animals, respectively, P = 0.009) and in saturated (P = 0.019) and monounsaturated fatty acid proportions (P = 0.044). The statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR < 0.10), 102 upregulated in IB and 154 upregulated in DU×IB. Transcript differences were validated for a subset of DE genes by qPCR. We observed alteration in biological functions related to extracellular matrix function and organization, cellular adhesion, muscle growth, lipid metabolism and proteolysis. Candidate genes with known effects on muscle growth were found among the DE genes upregulated in DU×IB. Genes related to lipid metabolism and proteolysis were found among those upregulated in IB. Regulatory factors (RF) potentially involved in the expression differences were identified by calculating the regulatory impact factors. Twenty-nine RF were found, some of them with known relationship with tissue development (MSTN, SIX4, IRX3), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these RF and DE genes show relevant differences between genetic types.ConclusionThese results provide valuable information about genetic mechanisms determining the phenotypic differences on growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. Transcription factors and regulatory mechanisms are proposed for these altered biological functions.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-413) contains supplementary material, which is available to authorized users.
Highlights
The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages
The main altered functional patterns observed with the different tools are discussed individually below: Tissue development and extracellular matrix (ECM) organization Among the differentially expressed (DE) genes affected by genetic type we found several widely known ones related to muscle development, including IGF2, which is the most significant DE gene with seven probes showing differential expression
Among the Regulatory factors (RF) predicted in the global study of DE genes and in each functional NW, we found RF which consistently appear with elevated Regulatory Impact Factor (RIF) z-scores in all analyses (MSTN, MXI1, SIX4, EYA2, Iroquois Homeobox 3 gene (IRX3) and ZHX2), which may be responsible of a large part of the gene expression differences detected in muscles from crossbred and purebred Iberian piglets
Summary
The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. Research on muscle lipid deposition is currently one of the most important fields of study in meat science [3]. The research interest on this topic includes the complex physiological and genetic mechanisms of IMF deposition and gene expression patterns and interactions along development [4]. IMF is considered a late-developing depot because hyperplasia and hypertrophy occurs postnatally, as demonstrated in both pigs and cattle [6,7]; and hypertrophy by lipid filling of adipocytes persists in late stages [8]. The adipocyte depots can be regulated differently, and may have a different propensity to metabolize lipids
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